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Estimated time of infection vs. confirmed infections

Following the ideas from Tomas Pueyo's Medium post "Coronavirus: Why You Must Act Now" [1], we assume the average time from infection to death at 23 days [2]. The data is pulled from the COVID-19 Data Repository by Johns Hopkins CSSE [3] every hour. Countries with a minimnum of 1000 confirmed cases and 40 confirmed deaths are included in this analysis.

The time from infection to death is equal to the incubation period plus the time from symptoms to death. This is used to estimate the time of the infections that lead to the observed deaths. We take the last fatality rate per country (total_cases/total_deaths) to estimate the number of infections that are responsible for the observed deaths.

In the figures below, you can observe successive waves of infections (dashed), detections (black) and deaths (red) for each country. The upper panel shows the absolute number of events. The dashed lines show the estimated number of infections. The lower panel shows the normalized number of events. Here the temporal delay between the waves and the relative change between each other can be observed.

[1] https://medium.com/@tomaspueyo/coronavirus-act-today-or-people-will-die-f4d3d9cd99ca

[2] https://github.com/midas-network/COVID-19/tree/master/parameter_estimates/2019_novel_coronavirus

[3] https://github.com/CSSEGISandData/COVID-19/tree/master/csse_covid_19_data/csse_covid_19_time_series

US
Brazil
India
Russia
Mexico
Peru
United Kingdom
Italy
Indonesia
Colombia
France
Iran
Argentina
Germany
Ukraine
Poland
South Africa
Spain
Turkey
Romania
Philippines
Hungary
Chile
Vietnam
Czechia
Canada
Ecuador
Bulgaria
Malaysia
Pakistan
Belgium
Bangladesh
Tunisia
Iraq
Greece
Egypt
Thailand
Netherlands
Bolivia
Portugal
Japan
Burma
Kazakhstan
Slovakia
Paraguay
Guatemala
Sweden
Sri Lanka
Morocco
Georgia
Bosnia and Herzegovina
Croatia
Austria
Serbia
Jordan
Switzerland
Nepal
Moldova
Honduras
Lebanon
Israel
Azerbaijan
Saudi Arabia
North Macedonia
Cuba
Armenia
Lithuania
Panama
Costa Rica
Afghanistan
Ethiopia
South Korea
Uruguay
Algeria
Ireland
Belarus
Libya
Slovenia
Kenya
Venezuela
Zimbabwe
West Bank and Gaza
Latvia
China
Australia
Dominican Republic
Oman
Denmark
Namibia
El Salvador
Zambia
Sudan
Uganda
Trinidad and Tobago
Albania
Nigeria
Kosovo
Syria
Cambodia
Kyrgyzstan
Jamaica
Montenegro
Botswana
Malawi
Kuwait
United Arab Emirates
Mozambique
Finland
Mongolia
Yemen
Estonia
Senegal
Cameroon
Angola
Uzbekistan
Norway
Rwanda
Bahrain
Ghana
Eswatini
Somalia
Congo (Kinshasa)
Madagascar
Suriname
Guyana
Mauritania
Luxembourg
Singapore
Haiti
Taiwan*
Fiji
Tanzania
Cote d'Ivoire
Mauritius
Cyprus
Bahamas
Mali
Lesotho
Qatar
Belize
Papua New Guinea
Laos
Malta
Guinea
Cabo Verde
Burkina Faso
Congo (Brazzaville)
Gambia
Saint Lucia
Gabon
Barbados
Maldives
Togo
Nicaragua
Hong Kong
Grenada
Djibouti
Equatorial Guinea
Benin
Seychelles
Andorra
South Sudan
Tajikistan
Timor-Leste
Central African Republic
San Marino

Ahead of the curve

Some countries start testing the population earlier in the outbreak than others. The time delay between the wave of deaths and the wave of confirmed cases is indicative for how early a country is detecting new cases ahead of the increase of deaths. Earlier detection means a better chances for successful isolation of an infected person and treatment of the desease.

We measure the distance of the maximum of cumulative deaths and new deaths to the number of infections to estimate the progression of the infection across countries.

If, in the early phase of the infection wave, the number of deaths rises faster than the number of confirmed cases, the distance drops, indicating that

A comparison of countries with respect to their mean time for reponse is presented below.

To determine the above values, we plot the number of confirmed cases (solid black lines) and the number of deaths (dashed black lines). From this, we measure the distance of the day of maximum deaths (dashed red lines) to the day of confirmed cases at this y-value.

The distance is indicative for how fast the humber of confirmed cases increases comapred to the increase of the number of deaths.

US
Brazil
India
Russia
Mexico
Peru
United Kingdom
Italy
Indonesia
Colombia
France
Iran
Argentina
Germany
Ukraine
Poland
South Africa
Spain
Turkey
Romania
Philippines
Hungary
Chile
Vietnam
Czechia
Canada
Ecuador
Bulgaria
Malaysia
Pakistan
Belgium
Bangladesh
Tunisia
Iraq
Greece
Egypt
Thailand
Netherlands
Bolivia
Portugal
Japan
Burma
Kazakhstan
Slovakia
Paraguay
Guatemala
Sweden
Sri Lanka
Morocco
Georgia
Bosnia and Herzegovina
Croatia
Austria
Serbia
Jordan
Switzerland
Nepal
Moldova
Honduras
Lebanon
Israel
Azerbaijan
Saudi Arabia
North Macedonia
Cuba
Armenia
Lithuania
Panama
Costa Rica
Afghanistan
Ethiopia
South Korea
Uruguay
Algeria
Ireland
Belarus
Libya
Slovenia
Kenya
Venezuela
Zimbabwe
West Bank and Gaza
Latvia
China
Australia
Dominican Republic
Oman
Denmark
Namibia
El Salvador
Zambia
Sudan
Uganda
Trinidad and Tobago
Albania
Nigeria
Kosovo
Syria
Cambodia
Kyrgyzstan
Jamaica
Montenegro
Botswana
Malawi
Kuwait
United Arab Emirates
Mozambique
Finland
Mongolia
Yemen
Estonia
Senegal
Cameroon
Angola
Uzbekistan
Norway
Rwanda
Bahrain
Ghana
Eswatini
Somalia
Congo (Kinshasa)
Madagascar
Suriname
Guyana
Mauritania
Luxembourg
Singapore
Haiti
Taiwan*
Fiji
Tanzania
Cote d'Ivoire
Mauritius
Cyprus
Bahamas
Mali
Lesotho
Qatar
Belize
Papua New Guinea
Laos
Malta
Guinea
Cabo Verde
Burkina Faso
Congo (Brazzaville)
Gambia
Saint Lucia
Gabon
Barbados
Maldives
Togo
Nicaragua
Hong Kong
Grenada
Djibouti
Equatorial Guinea
Benin
Seychelles
Andorra
South Sudan
Tajikistan
Timor-Leste
Central African Republic
San Marino